The Doctor's Soul
by bulmablue-eyes
Summary: After discovering a room in the TARDIS containing only a locked box and a bloodstained notebook, Amy's curiosity leads to the discovery of the Doctor's deepest and darkest secret.


**The Doctor's Soul**

Summary: After discovering a room in the TARDIS containing only a locked box and a bloodstained notebook, Amy's curiosity leads to the discovery of the Doctor's deepest and darkest secret.

Warnings: This story contains triggering images and scenes of self-harm.

Amy walked slowly and quietly through the TARDIS, her fingers trailing across the walls as she slowly wandered through the silent halls. It was the middle of the night (or would have been had they been on Earth), and, after spending much of her first night of married life unable to sleep, Amy had decided to walk around the TARDIS in an attempt to clear her head.

All of her newly recovered memories of the Doctor were flying through her mind at an alarming rate, always falling back onto horror at how readily the Time Lord was willing to sacrifice his own life. With the Daleks, the Angels, and, finally, with the Pandorica, it had seemed as though his first instinct was to sacrifice himself in order to save the world. And Amy had only known him for one of the 908 years of his life. How many more times had he been willing to sacrifice himself? _Why _did he seem so keen to die for others?

Amy was jolted out of her thoughts when she found herself in the console room, staring up at a door she had somehow failed to notice. Looking around the console room, Amy found herself reluctant to look back at the door, her eyes protesting as she forced herself to return her gaze.

"Perception filter." Amy whispered to herself under her breath. "But why would there be a perception filter?"

It was a plain door, slightly hidden in an alcove that shrouded it in shadows. Amy's eyes widened and her eyebrows furrowed when she glanced down at the door's handle, and noticed a patch of dried blood marring the otherwise unmarked metal.

Glancing briefly around the console room once more, making sure she was truly alone, Amy took a deep breath and grabbed the handle, opening the door and stepping into the mysterious room.

At first it appeared that the room was empty. After a moment though, Amy's eyes fell upon a wooden box in the corner of the room, locked with a heavy metal padlock, and on top of which sat a plain brown leather-bound book.

Amy stepped forwards, sliding lowering herself down to sit cross-legged in front of the box, and hesitating only briefly, reached forwards to take the notebook. A startled gasp fell from her lips as she picked the book up, turning it over to examine the cover. Dried blood was smeared across the thick leather cover, some patches new and smooth, the rich rust colour of recently dried blood, while other patches were darker and cracked with age.

Expelling a shaky breath, Amy opened the book, flicking through the thick, bloodstained pages. The book was filled with drawings of different people, with drops and smears of blood staining the paper, and below each drawing, in the Doctor's usual messy scribble was a name. Amy flicked slowly through each page, stopping to stare at each drawing and read the names accompanying them: Jabe Ceth Ceth Jafe, Gwyneth, Lynda, Davitch Pavale, the Controller, Sir Robert MacLeish, Angela Price, Ricky Smith, Ursula Blake, Colin Skinner, Bridget Sinclair, the Face of Boe, Dalek Sec, Kathryn McDonnell, John Smith, Mr Rocastle, Mr Phillips, Mr Chambers, Chantho, Captain Jack Harkness, Foon van Hoff, Bannakaffalatta, Astrid Peth, Luke Rattigan, Jenny, River Song, the Hostess, Harriet Jones, Captain Adelaide Brooke, The Master, Father Octavian, Isabella, Guido, Rory Williams.

Thirty three names. Who were they all? Only a couple of them were familiar. Amy's eyes brimmed with tears as she went back again to the beginning of the book, reading the notes that had been scribbled randomly on some of the pages. Next to the image of John Smith (a sad looking man with a bow tie and spiky dark hair), the Doctor had written shakily 'I created his life with the intention of stealing it away from him', and next to Jenny (a beautiful fair-haired girl around Amy's age) he had written 'A father should die for his child, not the other way around'.

The image of River Song made Amy's breath stutter in her throat, and her fingers ghosted gently over the Doctor's words: 'How can I face her, always knowing how she's going to die?'.

After several minutes, Amy found herself staring once again at the drawing of Rory. Amy's Rory, her husband, staring up at her from beneath drips and smears of blood, along with the words 'He didn't even like me' and 'Why? She chose him!'. Amy sighed, stroking her fingers over her husband's face, before jumping slightly as the lights in the room brightened suddenly before returning to their original intensity.

Amy stood quickly, placing the book carefully back on top of the box, before tiptoeing quietly out of the room and closing the door behind her.

Amy stepped up to the TARDIS console, leaning forwards against it seconds before the Doctor strolled into the room.

"Pond!" he exclaimed brightly, clapping his hands happily and making Amy jump in alarm. "What are you doing up and about this fine night?"

"Couldn't sleep." Amy replied, confused eyes following the Doctor as he hopped cheerfully around the console. "Just decided to take a stroll."

"Couldn't sleep, eh?" The Doctor repeated. "Tell you what I recommend. I recommend chocolate gateau and a film. What do you say? I'll get the gateau, you just stay right there and think of a film."

Amy nodded slowly, staring after the Doctor as he twirled around on the spot, clicked his fingers and practically bounced down the corridor towards the kitchen. How could this be the same person who had written such sad, heartbroken thoughts down in an old bloodstained journal?

Shaking her head, Amy started wandering around the console. Best forget about that for now. The Doctor had told her to think of a film.

Amy and Rory followed the Doctor into the TARDIS, leaning heavily against the wall to catch their breath while the Doctor hit button after button on the console, flying the TARDIS into space.

They had spent the day in Cardiff in the year 2316, where a group of red humanoid aliens had taken control of a warehouse, and were trying to use the staff to tear open the Rift and use it's energy to destroy all life on Earth and claim the planet for themselves. The Doctor had succeeded in stopping their plan, but, sadly, a young worker called Michael Willis, who had been working in the warehouse during the university holidays, had been killed, throwing himself into the path of a bullet aimed at the Doctor.

"Right then, Mr and Mrs Pond!" The Doctor said, grabbing Amy and Rory by the elbows and pulling them over to sit next to the console. "Let's just float around space for a bit while we catch our breaths, and then how about a trip to Egypt? I've always wanted to see how they built the pyramids. I bet they used sky-hooks!"

"Sounds good." Rory said, slipping an arm around Amy's shoulder. "Doesn't it Amy?"

"Yeah, sounds great." Amy replied, watching the Doctor carefully. His eyes kept drifting to look behind his companions, shooting rapidly between them and the door to the mysterious room with the box and the notebook.

"Good!" The Doctor said, grinning manically. "That's decided then. Now, if you don't mind, I'll just leave you two here for a bit, while I go do some... stuff."

Amy watched, her eyes narrowed, as the Doctor rushed quickly over to the hidden door, seeming to breathe a sigh of relief before slipping quietly into the room. Rory was talking animatedly about something, but Amy was too distracted by the silent debate going on in her mind. If she followed the Doctor into that room, she could find out what was in that box, but, on the other hand, he obviously didn't want anyone to find out, or he wouldn't have hidden the room behind a perception filter.

She had just decided to stay out in the console room, away from the Doctor's potential fury, when an image of the notebook floated up into her mind. All that blood. Where had all the blood come from? This could be a chance to find out. Nodding determinedly, Amy stood up.

"Back in a minute." She said absently to Rory. "You just wait here."

Amy opened the door quietly, letting herself slip carefully into the room. Once inside, however, she couldn't stop the shocked gasp that fell from her lips.

The Doctor's jacket had been thrown carelessly onto the floor next to the door, and he was currently sitting cross-legged, much as Amy herself had done, on the floor next to the box. The diary lay open on a blank page in front of him, the name 'Michael Willis' written at the top of the page in black ink. His sleeves had been rolled up to his elbows, and, as Amy watched silently, he lay his forearm out in front of him, and drew a razor blade across the skin of his inner arm in a vicious, angry swipe.

Blood oozed immediately from the wound, trickling in crimson rivulets down his arm and dripping onto the floor in front of him. Taking a deep breath, the Doctor nodded in apparent satisfaction, wiped the blade on a cloth, and dropped it back into the box.

A tear spilled from Amy's eye, rolling sadly down her cheek. Staring wide-eyed at the scene in front of her, she stepped forward slowly, taking a deep breath.

"Doctor?"

The Doctor's head snapped round to look at Amy, and he jumped to his feet, his face ashen and his eyes expressionless as he stared at her.

"Amy," he said, his voice calm and steady. "What are you doing here?"

"I followed you." She said, growing nervous at the deliberate and tenuous calm he was portraying. The cold steel in his eyes stared right through her, showing how desperately he was trying to keep hold of his emotions.

"I would have thought," he said slowly, his hands clenching at his side, blood dripping onto the floor, "given the presence of a perception filter, that it was quite clear to you that _THIS ROOM IS PRIVATE_!"

The last words were roared at Amy, any grip he may have had on his emotions clearly giving way. He span around on the spot, pacing around the room, stopping and random points before changing direction, refusing to even look at Amy.

"I found it accidentally last night." Amy told him, stepping forwards towards him.

"Get out."

Amy stared, her jaw dropping slightly. "No." She said calmly, glancing quickly down at his bleeding arm.

"I SAID GET OUT!" The Doctor spun around to face Amy, reaching forwards, as if to physically throw her from the room.

"And I said no." Amy replied stepping forward until she was barely two feet away from him. "I'm not leaving until you tell me what's going on. Why are you doing this?"

"Why do you want to know?" The Doctor asked, raising his eyes to look into Amy's.

"Because I care about you." Amy said, staring at him. "I want to understand why you're doing this to yourself."

"It's the least I can do." The Doctor whispered, looking away to stare absently at the notebook.

"Why?"

"Did you look in the journal last night?" He asked, bringing his gaze back to Amy's face. All of the anger had drained from his face, replaced instead by a deep, gut-wrenching sadness that seemed to reach deep into Amy and take her breath away. "I won't be angry."

"Yes." Amy replied, walking past the Doctor to sit down on the floor next to the box. "And I don't understand."

The Doctor sighed, before walking over and sitting down opposite Amy, picking up the notebook and flicking sadly through its pages. "The book is all the people who have died for me."

Amy stared, rolling this over and over in her mind before, slowly, oh so carefully, reaching forwards and taking the Doctor's hand. After waiting a moment to allow him to refuse, she pulled his hand towards her, turning his arm so that she could quietly survey his skin.

"Thirty four." She said after a moment. "That cut made it thirty four. You have one scar for every person to die for you."

"Yes." The Doctor confirmed quietly. "Every person to die for my since the war is remembered in that book. And... like this."

"But why hurt yourself?" Amy asked, turning her tearful eyes up to the Doctor's face. "They died for you. They wouldn't want this."

"BECAUSE THEY SHOULDN'T HAVE DIED!" The Doctor shouted, pulling his arm away from Amy and rubbing his hands frantically through his hair with a mumbled "Sorry."

"No, they shouldn't." Amy said, her eyes drifting briefly to the streaks of blood now left in the Time Lord's hair. "But it was their choice."

The Doctor stared, and Amy leaned forwards, pulling her once imaginary friend into her arms, hugging him close. "You can't save everyone, Doctor." She said quietly into his hair, feeling him slip his arms around her and hold her tightly to him. "I know you, and I know you'll always try, but that's why people are willing to die for you. Even you can't save everyone, but people know that a person who's willing to try is worth dying for."

"Someone once said to me" the Doctor began, his voice hesitant and shaking with tears, "that I'm the man who keeps running, never looking back because I dare not, out of shame. Because of all the people who have died for me, in my name." He took a deep breath, hiccuping slightly as, Amy realised, his first tears fell. "But I've done terrible things, Pond. I've committed genocide. Against the Daleks, the Saturnians. Even my own people. I abandoned Jack alone in the year 200100 because he had become something 'wrong'. And I became so arrogant, so determined not to lose, that I forced a woman to commit suicide to undo the damage I had done to the future of the human race. How can you _possibly_ say I'm somebody worth dying for?"

Amy hesitated, trying to match the acts the Doctor had described with the image of her raggedy Doctor. "Because despite all of that, you are still a good man. The best man. Everybody does things they regret. Everybody makes mistakes. But you're the Doctor. The things you regret and your mistakes have the potential to be catastrophic. You would only become somebody not worth dying for if you stopped seeing things like that as regrets and mistakes, and started doing them as a matter of course, just because you can."

Amy clenched her eyes closed, tears cascading down her face as she felt the Doctor sob into her shoulder.

"Oh, Amy." The Doctor sighed, burying his face in her hair. "I don't know what to do."

"I can't tell you what to do, Doctor." Amy told him. "I could say destroy that book, and don't ever do this again, but that would be pointless." She sighed deeply, stroking the Doctor's hair gently. "Just, promise me something."

"What?"

"Next time, don't hide." The Doctor pulled back slightly, searching Amy's face, looking for something in her eyes. "Talk to me. Even if you just come to talk, or to say 'Hey, Amy, I've done this'. There's too much guilt and self-blame, even for a Time Lord to take. It'll just make you hate yourself if you try to keep it all to yourself."

The Doctor stared at her for a moment, considering her words, before nodding silently.

"Thank you." Amy said, standing up and holding her hand out for the Doctor to take. "Now come with me. Let me help you take care of that cut."

The Doctor took her hand and pulled himself to his feet. Standing in front of her, eyes showing all of his nine-hundred and eight years staring deeply into hers, he leant forwards and kissed her gently on the lips, a soft, thankful peck, before pulling back.

"I'm sorry, Pond." He said quietly, smiling sadly at her.

"What for?" She asked.

"For shouting." He replied, squeezing her hand. "For getting so angry. This new regeneration is quite awkward with emotions. I don't know how to... you know. I seem to feel so much more than any of my other regenerations did. I don't know what to do with that."

"It's ok." Amy assured him, pulling him close into another tight hug. "I already figured you were a bit emotionally stunted."

The Doctor laughed slightly, burying his face once again in Amy's neck, mumbling quietly into her skin: "Gotcha".

_Fin._


End file.
